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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 819/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.37.0  (landing page)
Zachary Skidmore
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/GenVisR
git_branch: devel
git_last_commit: 3b6df4f
git_last_commit_date: 2024-04-30 10:47:51 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for GenVisR on palomino6

To the developers/maintainers of the GenVisR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenVisR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GenVisR
Version: 1.37.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenVisR_1.37.0.tar.gz
StartedAt: 2024-07-16 00:22:53 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 00:33:42 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 648.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GenVisR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenVisR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenVisR_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/GenVisR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.37.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'GenVisR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildWaterfallPlot,WaterfallData: no visible global function definition
  for 'tail'
setTierTwo,data.table: no visible global function definition for 'tail'
setTierTwo,data.table : a: no visible binding for global variable 'tmp'
toLolliplot,GMS: no visible binding for global variable 'missingINdex'
Undefined global functions or variables:
  missingINdex tail tmp
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) lohSpec.Rd:46: Lost braces; missing escapes or markup?
    46 | consisting of elements from the set {"M", "F"}. Used to suppress the plotting
       |                                     ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
Lolliplot-class 22.54   1.65  119.54
genCov           6.59   0.40    7.00
geneViz          6.50   0.11    6.61
cnSpec           6.34   0.10    6.56
cnFreq           5.01   0.01    5.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/GenVisR.Rcheck/00check.log'
for details.


Installation output

GenVisR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GenVisR
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'GenVisR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenVisR)

Tests output

GenVisR.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GenVisR)
> 
> test_check("GenVisR")
[ FAIL 0 | WARN 9 | SKIP 54 | PASS 510 ]

══ Skipped tests (54) ══════════════════════════════════════════════════════════
• On Bioconductor (54): 'test-Lolliplot-class.R:564:5',
  'test-Lolliplot-class.R:574:6', 'test-Lolliplot-class.R:602:5',
  'test-Lolliplot-class.R:615:5', 'test-Lolliplot-class.R:626:5',
  'test-Lolliplot-class.R:641:5', 'test-Lolliplot-class.R:654:5',
  'test-Lolliplot-class.R:730:5', 'test-Lolliplot-class.R:740:5',
  'test-Lolliplot-class.R:778:5', 'test-MutSpectra-class.R:285:5',
  'test-MutSpectra-class.R:294:5', 'test-MutSpectra-class.R:303:5',
  'test-MutSpectra-class.R:336:5', 'test-MutSpectra-class.R:345:5',
  'test-MutSpectra-class.R:354:5', 'test-MutSpectra-class.R:405:5',
  'test-MutSpectra-class.R:413:5', 'test-MutSpectra-class.R:440:5',
  'test-MutSpectra-class.R:450:5', 'test-Rainfall-class.R:247:5',
  'test-Rainfall-class.R:255:5', 'test-Rainfall-class.R:263:5',
  'test-Rainfall-class.R:297:5', 'test-Rainfall-class.R:305:5',
  'test-Rainfall-class.R:348:5', 'test-Rainfall-class.R:355:5',
  'test-Rainfall-class.R:389:5', 'test-Waterfall-class.R:662:5',
  'test-Waterfall-class.R:670:5', 'test-Waterfall-class.R:678:5',
  'test-Waterfall-class.R:686:5', 'test-Waterfall-class.R:722:5',
  'test-Waterfall-class.R:733:5', 'test-Waterfall-class.R:741:5',
  'test-Waterfall-class.R:750:5', 'test-Waterfall-class.R:758:5',
  'test-Waterfall-class.R:794:5', 'test-Waterfall-class.R:808:5',
  'test-Waterfall-class.R:819:5', 'test-Waterfall-class.R:830:5',
  'test-Waterfall-class.R:841:5', 'test-Waterfall-class.R:852:5',
  'test-Waterfall-class.R:868:5', 'test-Waterfall-class.R:906:5',
  'test-Waterfall-class.R:991:5', 'test-Waterfall-class.R:1005:5',
  'test-Waterfall-class.R:1019:5', 'test-Waterfall-class.R:1033:5',
  'test-Waterfall-class.R:1048:5', 'test-Waterfall-class.R:1062:5',
  'test-Waterfall-class.R:1076:5', 'test-Waterfall-class.R:1105:5',
  'test-Waterfall-class.R:1122:5'

[ FAIL 0 | WARN 9 | SKIP 54 | PASS 510 ]
Deleting unused snapshots:
• Lolliplot-class/drawplot-lolliplot.svg
• Lolliplot-class/final-lolliplot-alter-section-height.svg
• Lolliplot-class/final-lolliplot-base.svg
• Lolliplot-class/lolliplot-density-plot-layer.svg
• Lolliplot-class/lolliplot-density-plot.svg
• Lolliplot-class/lolliplot-plot-base-add-domain-palette.svg
• Lolliplot-class/lolliplot-plot-base-add-labels.svg
• Lolliplot-class/lolliplot-plot-base-add-layer.svg
• Lolliplot-class/lolliplot-plot-base-add-mutation-palette.svg
• Lolliplot-class/lolliplot-plot-base.svg
• MutSpectra-class/drawplot-mutspectra.svg
• MutSpectra-class/final-mutspectra-alter-section-heights.svg
• MutSpectra-class/final-mutspectra-base.svg
• MutSpectra-class/mutspectra-clinical.svg
• MutSpectra-class/mutspectra-frequency-plot-add-layer.svg
• MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-frequency-plot.svg
• MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
• MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-proportion-plot.svg
• Rainfall-class/density-main-plot.svg
• Rainfall-class/density-plot-add-layer.svg
• Rainfall-class/drawplot-rainfall.svg
• Rainfall-class/final-rainfall-alter-section-hieghts.svg
• Rainfall-class/final-rainfall-base.svg
• Rainfall-class/rainfall-main-plot.svg
• Rainfall-class/rainfall-plot-add-layer.svg
• Rainfall-class/rainfall-plot-aesthetic-options.svg
• Waterfall-class/addgene-waterfall.svg
• Waterfall-class/drawplot-waterfall.svg
• Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
• Waterfall-class/final-waterfall-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg
• Waterfall-class/final-waterfall-and-top-sub-plot.svg
• Waterfall-class/final-waterfall-base.svg
• Waterfall-class/gene-plot-add-layers.svg
• Waterfall-class/gene-plot-frequency-complex.svg
• Waterfall-class/gene-plot-frequency-simple.svg
• Waterfall-class/gene-plot-proportion-complex.svg
• Waterfall-class/gene-plot-proportion-simple.svg
• Waterfall-class/main-waterfall-add-layers.svg
• Waterfall-class/main-waterfall-plot-base.svg
• Waterfall-class/main-waterfall-plot-drop-true.svg
• Waterfall-class/main-waterfall-plot-grid-true.svg
• Waterfall-class/main-waterfall-plot-label.svg
• Waterfall-class/main-waterfall-plot-samplenames-false.svg
• Waterfall-class/main-waterfall-plot-xtitle-false.svg
• Waterfall-class/mutation-plot-add-layers.svg
• Waterfall-class/mutation-plot-burden-complex.svg
• Waterfall-class/mutation-plot-burden-simple.svg
• Waterfall-class/mutation-plot-frequency-complex.svg
• Waterfall-class/mutation-plot-frequency-simple.svg
> 
> proc.time()
   user  system elapsed 
 105.48    7.89  186.92 

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class 22.54 1.65119.54
TvTi1.240.041.28
Waterfall-class0.500.040.53
cnFreq5.010.015.12
cnSpec6.340.106.56
cnView0.470.010.49
compIdent1.530.271.79
covBars0.630.000.64
genCov6.590.407.00
geneViz6.500.116.61
ideoView0.260.000.27
lohSpec3.610.063.65
lohView0.50.00.5